dbdicom 0.3.6__tar.gz → 0.3.7__tar.gz

{dbdicom-0.3.6/src/dbdicom.egg-info → dbdicom-0.3.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dbdicom
-Version: 0.3.6
+Version: 0.3.7
 Summary: A pythonic interface for reading and writing DICOM databases
 Author-email: Steven Sourbron <s.sourbron@sheffield.ac.uk>, Ebony Gunwhy <e.gunwhy@sheffield.ac.uk>
 Project-URL: Homepage, https://openmiblab.github.io/dbdicom/

{dbdicom-0.3.6 → dbdicom-0.3.7}/pyproject.toml

@@ -7,7 +7,7 @@ requires = ['setuptools>=61.2']
 
 [project]
 name = "dbdicom"
-version = "0.3.6"
+version = "0.3.7"
 dependencies = [ 
     "tqdm",
     "importlib-resources",

{dbdicom-0.3.6 → dbdicom-0.3.7}/src/dbdicom/api.py

@@ -1,10 +1,18 @@
+import os
+import shutil
+import zipfile
+from pathlib import Path
 from typing import Union
+from tqdm import tqdm
+
 
 import vreg
 
 from dbdicom.dbd import DataBaseDicom
 
 
+
+
 def open(path:str) -> DataBaseDicom:
     """Open a DICOM database
 
@@ -363,10 +371,74 @@ def unique(pars:list, entity:list) -> dict:
     return u
 
 
+def archive(path, archive_path):
+    dbd = open(path)
+    dbd.archive(archive_path)
+    dbd.close()
+
+
+def restore(archive_path, path):
+    _copy_and_extract_zips(archive_path, path)
+    dbd = open(path)
+    dbd.close()
 
 
+def _copy_and_extract_zips(src_folder, dest_folder):
+    if not os.path.exists(dest_folder):
+        os.makedirs(dest_folder)
 
+    # First pass: count total files
+    total_files = sum(len(files) for _, _, files in os.walk(src_folder))
 
-if __name__=='__main__':
+    with tqdm(total=total_files, desc="Copying and extracting") as pbar:
+        for root, dirs, files in os.walk(src_folder):
+            rel_path = os.path.relpath(root, src_folder)
+            dest_path = os.path.join(dest_folder, rel_path)
+            os.makedirs(dest_path, exist_ok=True)
 
+            for file in files:
+                src_file_path = os.path.join(root, file)
+                dest_file_path = os.path.join(dest_path, file)
+
+                if file.lower().endswith('.zip'):
+                    try:
+                        zip_dest_folder = dest_file_path[:-4]
+                        with zipfile.ZipFile(src_file_path, 'r') as zip_ref:
+                            zip_ref.extractall(zip_dest_folder)
+                        #tqdm.write(f"Extracted ZIP: {src_file_path}")
+                        #_flatten_folder(zip_dest_folder) # still needed?
+                    except zipfile.BadZipFile:
+                        tqdm.write(f"Bad ZIP file skipped: {src_file_path}")
+                else:
+                    shutil.copy2(src_file_path, dest_file_path)
+
+                pbar.update(1)
+
+
+def _flatten_folder(root_folder):
+    for dirpath, dirnames, filenames in os.walk(root_folder, topdown=False):
+        for filename in filenames:
+            src_path = os.path.join(dirpath, filename)
+            dst_path = os.path.join(root_folder, filename)
+            
+            # If file with same name exists, optionally rename or skip
+            if os.path.exists(dst_path):
+                base, ext = os.path.splitext(filename)
+                counter = 1
+                while os.path.exists(dst_path):
+                    dst_path = os.path.join(root_folder, f"{base}_{counter}{ext}")
+                    counter += 1
+
+            shutil.move(src_path, dst_path)
+
+        # Remove empty subdirectories (but skip the root folder)
+        if dirpath != root_folder:
+            try:
+                os.rmdir(dirpath)
+            except OSError:
+                print(f"Could not remove {dirpath} — not empty or in use.")
+
+
+
+if __name__=='__main__':
     pass

{dbdicom-0.3.6 → dbdicom-0.3.7}/src/dbdicom/dbd.py

@@ -2,6 +2,7 @@ import os
 from datetime import datetime
 import json
 from typing import Union
+import zipfile
 
 from tqdm import tqdm
 import numpy as np
@@ -880,6 +881,34 @@ class DataBaseDicom():
         register.add_instance(self.register, attr, rel_path)
 
 
+    def archive(self, archive_path):
+        # TODO add flat=True option for zipping at patient level
+        for pt in tqdm(self.register, desc='Archiving '):
+            for st in pt['studies']:
+                zip_dir = os.path.join(
+                    archive_path,
+                    f"Patient__{pt['PatientID']}", 
+                    f"Study__{st['StudyID']}__{st['StudyDescription']}", 
+                )
+                os.makedirs(zip_dir, exist_ok=True)
+                for sr in st['series']:
+                    try:
+                        zip_file = os.path.join(
+                            zip_dir, 
+                            f"Series__{sr['SeriesNumber']}__{sr['SeriesDescription']}.zip",
+                        )
+                        with zipfile.ZipFile(zip_file, 'w') as zipf:
+                            for rel_path in sr['instances'].values():
+                                file = os.path.join(self.path, rel_path)
+                                zipf.write(file, arcname=os.path.basename(file))
+                    except Exception as e:
+                        raise RuntimeError(
+                            f"Error extracting series {sr['SeriesDescription']} "
+                            f"in study {st['StudyDescription']} of patient {pt['PatientID']}."
+                        )
+
+
+
 
 def infer_slice_spacing(vols):
     # In case spacing between slices is not (correctly) encoded in 

{dbdicom-0.3.6 → dbdicom-0.3.7/src/dbdicom.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dbdicom
-Version: 0.3.6
+Version: 0.3.7
 Summary: A pythonic interface for reading and writing DICOM databases
 Author-email: Steven Sourbron <s.sourbron@sheffield.ac.uk>, Ebony Gunwhy <e.gunwhy@sheffield.ac.uk>
 Project-URL: Homepage, https://openmiblab.github.io/dbdicom/